Supplementary Table 1 Compound databases used for virtual screening

Database name / Number of compounds:
unfiltered / Number of compounds: filtered
Agro / 80 / 23
Chemdivision 1 / 100 000 / 30 041
Chemdivision 2 / 100 000 / 48 659
Genplus / 960 / 103
Killer A / 80 / 21
Killer B / 80 / 36
Maybridge / 60 000 / 14 365
Natprod / 720 / 145
NATx / 5 052 / 1 270
NCI / 250 251 / 9 817
Spectrum / 2 000 / 571
Timtec / 121 824 / 8 537
Cancer / 80 / 21
Total / 641 127 / 113 609

Supplementary Table 2 DOCK v 5.1.1 ligand parameters.

ligand_atom_file / ligand_concord.mol2
ligand_outfile_prefix / ligand_out
write_orientations / yes
write_conformations / yes
calculate_rmsd / yes
rank_ligands / no
max_send_queue_size / 10
max_recv_queue_size / 10 000
orient_ligand / yes
automated_matching / yes
receptor_site_file / pro.sph
max_orientations / 1000
flexible_ligand / yes
min_anchor_size / 10
number_confs_per_cycle / 50
use_clash_overlap / no
anchor_rmsd_clustering / no
bump_filter / yes
bump_grid_prefix / pro
max_bumps / 3
score_molecules / yes
contact_score_primary / no
contact_score_secondary / no
energy_score_primary / yes
energy_score_secondary / yes
vdw_scale / 1
es_scale / 1
nrg_grid_prefix / pro
minimize_ligand / yes
minimze_rigid_anchor / yes
minimze_layer_growth / yes
minimze_final_pose / yes
minimze_final_pose_rigid / no
minimze_final_pose_torsions / no
minimize_final_pose_complete / yes
minimizer_choice / 0
initial_translation / 1
initial_rotation / 1
initial_torsion / 10
use_rotational_minimizer / no
maximum_iterations / 100
maximum_function_calls / 100 000
window_based_termination / no
scaled_range_termination / no
multiple_simplex_cycles / no
random_number_generator / 0
random_number_seed / 2002
calc_internal_energy / no
atom_model / all
vdw_defn_file / vdw.defn
flex_defn_file / flex.defn
flex_drive_file / flex_drive.tbl

Supplementary Table 3 DOCK v 5.1.1 protein parameters

compute_grids / yes
grid_spacing / 0.3
output_molecule / no
contact_score / yes
contact_cutoff_distance / 4.5
chemical_score / yes
energy_score / yes
energy_cutoff_distance / 5
atom_model / u
attractive_exponent / 6
repulsive_exponent / 12
distance_dielectric / yes
dielectric_factor / 4
bump_filter / yes
bump_overlap / 0.5
receptor_file / pro_syb.mol2
box_file / box.pdb
vdw_definition_file / vdw.defn
chemical_definition_file / chem.defn
score_grid_prefix / pro

Supplementary Table 4 GOLD docking parameters

Parameters / Library screening settings / 3-times-up settings / Standard settings
Population size / 50 / 100 / 100
Number of islands / 1 / 3 / 5
Niche size / 2 / 2 / 2
Selection pressure / 1.125 / 1.100 / 1.100
Migrate / 0 / 10 / 2
Number of operators / 1 000 / 30 000 / 100 000
Mutate / 100 / 95 / 95
Crossover / 100 / 95 / 95

Supplementary Table 5 Structures, database source and virtual screening results for the 41 compounds with GOLD fitness score >70. Compounds R1-R7 are indicated.

Chemical Structure / Database / GOLD fitness score / GOLD X-Score (kcal/mol) / FlexX binding energy (kcal/mol) / FlexX X-Score (kcal/mol) / DOCK binding energy (kcal/mol) / DOCK X-Score (kcal/mol)
R1
/ Chemdivison 2 / 71.72 / -9.43 / -18.06 / -7.52 / -5.83 / -7.31
R2
/ Chemdivison 2 / 71.75 / -8.42 / -19.82 / -7.38 / -9.44 / -6.64
R3
/ Chemdivison 2 / 77.42 / -9.21 / -15.93 / -7.04 / -8.39 / -7.03
R4
/ Chemdivison 2 / 70.11 / -8.79 / -13.91 / -7.44 / -11.58 / -7.92
R5
/ Chemdivison 2 / 71.93 / -8.66 / -14.35 / -6.61 / -10.74 / -6.63
R6
/ Chemdivison 2 / 72.29 / -8.68 / -17.06 / -7.13 / -11.03 / -6.94
R7
/ Timtec / 70.13 / -9.11 / -13.88 / -7.06 / -4.77 / -7.19

/ Killer A / 70.72 / -7.99 / 1.69 / -6.84 / -13.89 / -7.73

/ NATx / 70.29 / -8.64 / -21.95 / -8.72 / -7.92 / -6.82

/ NATx / 70.39 / -8.67 / -12.86 / -7.70 / -5.61 / 6.80

/ NATx / 70.39 / -7.23 / 19.58 / -6.99 / -11.83 / -6.57

/ NATx / 70.52 / -8.74 / -14.44 / -7.32 / -8.44 / -6.76

/ NATx / 70.94 / -8.48 / -23.12 / -8.85 / -8.31 / -6.37

/ NATx / 71.41 / -6.85 / -23.05 / -7.67 / -8.40 / -6.39

/ NATx / 71.45 / -7.70 / -16.32 / -8.56 / -8.98 / -7.81

/ NATx / 71.59 / -7.58 / -18.19 / -7.63 / -11.82 / -8.09

/ NATx / 71.73 / -7.57 / -21.46 / -6.95 / -10.09 / -6.84

/ NATx / 72.47 / -6.96 / -18.86 / -6.52 / -9.17 / -6.43

/ NATx / 72.73 / -8.04 / -15.86 / -8.75 / -13.00 / -8.12

/ NATx / 74.75 / -7.80 / -19.20 / -7.00 / -11.62 / -7.25

/ NATx / 75.76 / -7.93 / -13.45 / -7.43 / -9.56 / -8.23

/ NATx / 75.91 / -7.68 / -18.75 / -6.99 / -8.6 / -7.19

/ NATx / 77.01 / -7.78 / -9.41 / -7.41 / -0.34 / -7.50

/ NATx / 77.76 / -7.63 / -12.29 / -8.40 / -7.41 / -7.62

/ NATx / 78.32 / -8.57 / -15.48 / -8.92 / -8.056 / -6.96

/ Timtec / 73.80 / -9.47 / -14.22 / -7.50 / 20.14 / -8.55

/ Maybridge / 70.20 / -8.54 / -16.84 / -6.68 / -9.19 / -6.99

/ Maybridge / 71.34 / -8.12 / -15.98 / -7.24 / -10.33 / -6.87

/ Chemdivison 2 / 70.21 / -8.47 / -17.17 / -7.10 / -8.98 / -6.68

/ Chemdivison 2 / 70.47 / -8.71 / -14.03 / -6.72 / -9.09 / -7.16

/ Chemdivison 2 / 70.68 / -8.57 / -14.60 / -6.44 / -10.83 / -7.13

/ Chemdivison 2 / 71.05 / -8.51 / -12.64 / -6.71 / -12.07 / -7.64

/ Chemdivison 2 / 71.11 / -9.48 / -16.18 / -8.05 / -8.99 / -7.41

/ Chemdivison 2 / 71.28 / -8.60 / -13.84 / -6.69 / -9.41 / -6.79

/ Chemdivison 2 / 71.42 / -8.67 / -13.08 / -6.90 / -11.00 / -7.29

/ Chemdivison 2 / 71.73 / -8.70 / -16.23 / -6.53 / -9.95 / -7.16

/ Chemdivison 2 / 72.00 / -8.56 / -14.56 / -6.86 / -8.44 / -6.98

/ Chemdivison 2 / 72.25 / -8.65 / -14.10 / -6.93 / -10.33 / -6.64

/ Chemdivison 2 / 72.35 / -8.99 / -5.76 / -7.29 / 1548.84 / -7.48

/ Chemdivison 2 / 73.32 / -8.83 / -13.88 / -6.69 / -10.02 / -7.39

/ Chemdivison 2 / 75.33 / -9.38 / -12.23 / -8.16 / -4.95 / -7.32

Supplementary Table 6 Physicochemical properties of compounds R1-R7

Molecule / Molecular mass (Da) / Number of H-bond donors / Number of H-bond acceptors / Rotatable bond count / ClogP a / ClogD a
R1 / 414.8 / 1 / 5 / 5 / 5.82 / 5.88
R2 / 419.5 / 2 / 5 / 8 / 2.31 / 2.39
R3 / 420.5 / 2 / 7 / 6 / 5.23 / 0.86
R4 / 417.3 / 1 / 5 / 7 / 4.86 / 4.20
R5 / 373.5 / 2 / 6 / 8 / 3.69 / 3.91
R6 / 378.5 / 1 / 6 / 6 / 4.06 / 4.54
R7 / 418.4 / 3 / 8 / 4 / 4.21 / 3.83

a ClogP is the calculated value of the logarithm of the octanol/water partition coefficient, and ClogD is the calculated value of the logarithm of the octanol/water distribution coefficient. Calculated with the program MarvinView (ChemAxon).

Supplementary Table 7 Interactions of compounds R1-R7 with DENV2 E protein after docking with GOLD

Molecule / Residues forming hydrogen-bonds (number of bonds) / Number of other interacting residues / Close contacts (2.5-3.5 Å) / Percentage of close contacts / GOLD fitness score /

Xscore (kcal/mol)

R1 / Ser363 (1), Thr359 (1), Ser 145 (1) / 14 / 13 of 33 / 39.4 / 71.72 / -9.43
R2 / Ser363 (2), Ile357 (1), Ser145 (1) / 13 / 8 of 34 / 33 / 71.75 / -8.42
R3 / Tyr178 (1), Ser145 (1) / 13 / 10 of 36 / 27.7 / 77.42 / -9.21
R4 / Tyr178 (1) / 10 / 13 of 35 / 37 / 70.11 / -8.79
R5 / Ser363 (1), Ile357 (1), Glu147 (1), Ser 145(2) / 15 / 5 of 27 / 18.5 / 71.93 / -8.66
R6 / Ser363 (1), Ile357 (1), Asn355 (1), Ser145 (3) / 11 / 10 of 36 / 27.7 / 72.29 / -8.68
R7 / Ile357 (2), Ser363 (1), Ser145 (1) / 10 / 10 of 42 / 23.8 / 70.13 / -9.11

Supplementary Table 8 Interactions of compounds R1-R7 with envelope proteins of other flaviviruses after docking with GOLD

Protein (PDB ID) / Residues forming hydrogen-bonds / Number of other interacting residues / Close contacts (2.5–3.5 Å) / Percentage of close contacts / GOLD fitness score / X-Score (kcal/mol)
1OKE / Ser363, Thr359, Ser145 / 14 / 13 of 33 / 39.4 / 71.72 / -9.43
1OAN / Ser363, Glu360, Thr359 / 12 / 9 of 27 / 33.3 / 67.68 / -9.51
1UZG / Thr357, Val355, Thr145 / 11 / 11 of 35 / 31.43 / 52.53 / -8.49
1SVB / Tyr179, Glu178 / 8 / 8 of 22 / 36.4 / 60.28 / -9.04
2HG0 / - / 7 / 11 of 34 / 32.3 / 55.81 / -8.74
JEVa / Ser364, Phe360, Tyr155, Thr146, Gly145 / 11 / 13 of 44 / 29.5 / 53.13 / -9.09

a Japanese encephalitis E protein structure (Kolaskar and Kulkarni-Kale (1999) Virology 261:31).

Supplementary Fig. 1

Supplementary Fig. 1. Work-flow diagram of the virtual screening procedure used in this work.

1